Her son and party vice president Rahul Gandhi also expressed shock at the killing of the firebrand journalist in Bengaluru yesterday and said no one could suppress the truth.
The Congress president described Ms Lankesh as one with fearless and independent views, who had extraordinary grit and determination to take on the system.
"The series of killings of rationalists, free thinkers and journalists in the country has created an atmosphere that dissent, ideological differences and divergence of views can endanger our lives. This cannot be and should not be tolerated," Sonia Gandhi said in a statement.
"It is an extremely sad moment for our democracy and a chilling reminder of the fact that intolerance and bigotry is raising its ugly head in our society," she said.
In condemning this debilitating attack, the Congress party stands as one with the rationalists, thinkers, journalists and the media fraternity, she said.
Expressing her deepest condolences to Ms Lankesh's family and friends, the Congress president said she offered her prayers.
Rahul Gandhi attacked Prime Minister Narendra Modi and described him as a "skilled Hindutva politician", what he spoke had a different meaning for his base and another one for the world.
"No one can suppress the truth. The RSS and BJP ideology is trying to suppress the truth but this cannot happen in India," he told reporters in New Delhi.
Ms Lankesh, 55, known for her left-leaning outlook and forthright views on "Hindutva politics", was shot dead by unidentified assailants at her residence last evening.